Summary

Name:

1384: Solved Foldit Design: Electron Density

Status:

Closed

Created:

05/30/2017

Points:

100

Expired:

06/06/2017 - 23:00

Difficulty:

Intermediate

Description:

This puzzle features a protein designed from scratch by Foldit players! In Puzzle 1381 we asked players to try to predict the structure of this protein from the sequence alone. We have since solved the crystal structure of this protein, and here we are providing players with the refined electron density map. See the blog for more details. Players can load in solutions from Puzzle 1381 to see how their predictions fit in the electron density map, and players can try building into the electron density from an extended chain!

Thanks. The number is a bit surprising to me if I compare that with the resolution of the previous puzzle 1357 at 1.5A. Puzzle 1384 has quite a few stretches of the protein that don't show up at all. I guess it makes sense if it is the maximum resolution this number is referring to...
So, if I read in a paper "the structure of protein x has been determined at 1.5A resolution" what does that mean exactly? On average 1.5A? Maximum of 1.5A? 1.5A except in variable regions? I know it is probably a bit pedantic, I just haven't thought about this much before Foldit ED puzzles.

Good question! When we talk about resolution limits in x-ray crystallography, we're talking specifically about the extent of x-ray diffraction (see the blog for more on diffraction). With respect to the electron density map, the resolution limit is just that—a limit. A resolution limit of 1.5 Å means roughly that the raw data contain no information about positions closer than 1.5 Å.

Other effects can "blur" portions of the refined electron density map—mostly having to do with ambiguous atom placement (e.g. thermal motion, partial occupancy, disordered regions).

It seems odd to see a cloud with very clear outlines for interior atoms and no cloud whatsoever for whole residues (not just sidechains) at the protein surface. I can imagine the many long blue sidechains on the surface of a foldit design being floppy and maybe not having cloud, but I would not expect the very short loops in this protein to be disordered, would you? The complete lack of cloud for a tyrosine is also surprising. What is going on?

Another note - moving the threshold slider to the left usually shows more and more cloud, but in this puzzle a threshold of 0 shows the same as having it at a quarter of the slider - it's like the less-certain part of the cloud has been completely omitted.

Hmm, that's strange. In the full electron density map, all of the residues (and most of the sidechains) are well resolved. Something must have happened when we trimmed the density map for the Foldit puzzle. I'm sorry we didn't catch that before posting the puzzle!